Gene detail

Detailed information of OS493_009816-T1 in Lophelia pertusa

Genomic Location: scaffold_23:2948303...2968581
NR annotation: KAJ7363654.1, Paraspeckle component 1 [Desmophyllum pertusum]
Species Lophelia pertusa · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q1LZD9	Paraspeckle component 1 OS=Bos taurus OX=9913 GN=PSPC1 PE=2 SV=1
Q5ZK88	Paraspeckle component 1 OS=Gallus gallus OX=9031 GN=PSPC1 PE=2 SV=1
Q4KLH4	Paraspeckle component 1 OS=Rattus norvegicus OX=10116 GN=Pspc1 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003464 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF08075 all species →	NOPS	NOPS (NUC059) domain	Domain	Interproscan
PF00076 all species →	RRM_1	RNA recognition motif	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR000504 all species →	Domain	RNA recognition motif domain	Interproscan
IPR012975 all species →	Domain	NOPS	Interproscan
IPR012677 all species →	Homologous_superfamily	Nucleotide-binding alpha-beta plait domain superfamily	Interproscan
IPR035979 all species →	Homologous_superfamily	RNA-binding domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR23189 all species →	RNA RECOGNITION MOTIF-CONTAINING	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0003676 all species →	Molecular Function	nucleic acid binding	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan

Search by domain instead of by gene. Any accession above (InterPro, Pfam, PANTHER, GO, KEGG) can be used as a query on the Functional Domain Search page, which searches all 148 annotated genomes at once.

KEGG pathway

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K13219	SFPQ, PSF; splicing factor, proline- and glutamine-rich	-	Spliceosome	ko03041	deepkoala

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Expression pattern (RNA-seq)

Transcript abundance of OS493_009816-T1 across 110 RNA-seq samples of Lophelia pertusa. Values are TPM (transcripts per million) from the StringTie quantification; one bar is one sample, grouped and coloured by condition, sorted by expression within each group.

110Samples

110TPM > 0

7Conditions

139.9Max TPM

55.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	45.48	61.87
polyp at pH7 6	18	18	48.53	67.09
coral polyp · control treatment	16	16	65.03	128.13
coral polyp · oil and dispersant treatment	16	16	58.57	99.09
coral polyp · oil treatment	16	16	55.10	68.98
coral polyp · dispersant treatment	16	16	77.23	139.88
Polyp	10	10	34.83	47.80

Per sample · hover a bar for the full sample record · show / hide the sample table

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	61.87
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	52.13
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	50.75
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	49.34
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	48.61
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	48.55
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	47.28
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	47.11
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	46.91
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	45.15
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	45.03
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	44.13
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	44.01
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	41.33
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	39.88
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	37.22
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	35.96
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	33.38
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	67.09
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	59.59
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	55.68
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	55.44
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	55.21
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	54.22
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	51.64
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	49.09
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	47.83
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	47.34
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	46.66
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	46.57
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	43.43
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	43.19
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	42.64
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	36.79
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	35.64
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	35.49
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	128.13
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	89.30
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	83.44
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	78.54
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	65.11
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	64.97
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	63.51
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	63.09
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	61.05
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	56.25
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	55.53
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	53.88
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	52.94
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	48.31
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	43.61
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	32.74
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	99.09
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	71.33
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	70.69
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	68.86
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	63.46
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	62.60
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	58.86
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	56.69
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	53.81
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	51.87
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	51.43
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	50.84
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	49.04
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	44.31
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	43.96
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	40.23
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	68.98
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	64.13
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	62.69
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	61.78
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	60.42
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	57.77
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	57.23
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	55.52
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	55.37
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	53.13
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	52.89
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	52.34
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	50.07
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	49.17
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	41.87
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	38.28
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	139.88
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	114.34
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	96.23
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	91.83
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	89.46
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	82.51
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	79.09
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	78.50
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	72.99
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	70.95
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	68.25
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	64.05
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	60.22
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	59.59
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	37.13
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	30.72
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	47.80
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	46.13
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	40.80
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	38.05
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	36.72
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	34.40
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	28.39
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	28.01
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	26.57
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	21.45

Source: CnidoSite RNA-seq expression matrices (LPERT_TPM, StringTie quantification over 110 runs), joined to SRA sample metadata. Samples whose tissue/treatment is not recorded in the source metadata are grouped by the descriptor carried in the expression matrix itself.